When you play a character, you get to see the world through their eyes. Whether it's a fictional world or a real world, you do get to see somebody else's point of view, whether he's a good guy or a bad guy.
Sometimes stereotyping happens not because of any nefarious reasons but rather because people don't know who you are or where you come from, so they go for the broad strokes about you, your culture, your faith, all that.
When I read a script, if I feel it's written with the idea of just bashing other people, then I shy away from it. Sometimes it's some guy coming out with his own hatred, and I don't need to be a part of it.
I think you can do science fiction, but you have to ground it in some realism. People need to identify with the characters, with their plights and their issues.